Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

Andrew D. W. Geering (), Florian Maumus, Dario Copetti, Nathalie Choisne, Derrick J. Zwickl, Matthias Zytnicki, Alistair R. McTaggart, Simone Scalabrin, Silvia Vezzulli, Rod A. Wing, Hadi Quesneville and Pierre-Yves Teycheney
Additional contact information
Andrew D. W. Geering: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland
Florian Maumus: INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr
Dario Copetti: Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona
Nathalie Choisne: INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr
Derrick J. Zwickl: University of Arizona
Matthias Zytnicki: INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr
Alistair R. McTaggart: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland
Simone Scalabrin: Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine Luigi Danieli
Silvia Vezzulli: Research and Innovation Centre, Fondazione Edmund Mach
Rod A. Wing: Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona
Hadi Quesneville: INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr
Pierre-Yves Teycheney: CIRAD UMR AGAP, Station de Neufchâteau, Sainte-Marie

Nature Communications, 2014, vol. 5, issue 1, 1-11

Abstract: Abstract The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called ‘Florendovirus’, members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of Oryza is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20–34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In Vitis vinifera, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks.

Date: 2014
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DOI: 10.1038/ncomms6269

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